I attempted to submit this post as a non-member last week, but it never appeared on the list. I'm re-posting as a member now, hope it isn't a duplicate... I'm using the 'altcdfenv' package to create an alternative CDF environment for the "ATH1-121501" chip. We would like to re-do our analysis on 30 chips after removing about 15,000 probes. I'm first trying to succeed at creating a new CDF env by removing whole genes (or probe sets) from the analysis. It looks like I'm close(my new environment has the correct number of subsetted genes), but when I request the probe indices for a given gene using the new CDF environment 'env.ath.new.cdf' and the 'get' function, the information is returned as a list of length 22, instead of an 11x2 matrix as in the original CDF environment. > get(ls(env.ath.new.cdf)[1],env.ath.new.cdf) $"244901_at" [1] 501131 251604 261891 230387 217334 451116 488419 215764 92381 334408 53876 501843 252316 262603 231099 218046 [17] 451828 489131 216476 93093 335120 54588 ## Using the original CDF environment: > get(ls(ath1121501cdf)[1],ath1121501cdf) pm mm [1,] 501131 501843 [2,] 251604 252316 [3,] 261891 262603 [4,] 230387 231099 [5,] 217334 218046 [6,] 451116 451828 [7,] 488419 489131 [8,] 215764 216476 [9,] 92381 93093 [10,] 334408 335120 [11,] 53876 54588 This shape difference makes the suite of affy tools incompatible for the new CDF environment. I've followed the vignette for 'alternative CDF environments' and I've looked around the R-list, but I'm not sure where to go next. Somehow I've got to get the new CDF environment to see this list as a matrix or I'll end up with errors like: > indexProbes(cel.files.30.lines, which="pm", genenames="244901_at")[[1]] Error in ans[[i]][, i.probes] : incorrect number of dimensions Any suggestions? Thanks, Rhonda P.S. I've included the code for the creation of 'env.ath.new.cdf' below. _______________________________________________________________ R version 2.0.1 altcdfenv version 1.1-10 > ## Create an alternative CDF environment: > ath.old.cdf<-wrapCdfEnvAffy(ath1121501cdf,712,712,"ath1121501cdf") > ids<-geneNames(ath.old.cdf) > ids.subset<-ids[c(1,2,3)] > ath.new.cdf<-ath.old.cdf[ids.subset] > print(ath.new.cdf) > Instance of class CdfEnvAffy: name : ath1121501cdf-subset chip-type: ath1121501cdf size : 712 x 712 3 probe set(s) defined. > > env.ath.new.cdf<-as(ath.new.cdf,"environment") > > > > ## Load in the 30 cel files: > setwd("D:/Rhonda/Lall/2nd_experiment/cel_files") > cel.files.30.lines<-ReadAffy() > > ## Re-assign the cdf environment for the AffyBatch: > cel.files.30.lines@cdfName<-"env.ath.new.cdf" > > gn.new<-geneNames(cel.files.30.lines) > gn.new [1] "244901_at" "244902_at" "244903_at" > ls(env.ath.new.cdf) [1] "244901_at" "244902_at" "244903_at"